Changes to the act, making it legal for Australia to send asylum seekers to Nauru and Papua New Guinea for processing, passed the Senate late on Thursday after a marathon debate.

Australian Human Right Commission president Professor Gillian Triggs said the amendments, which had the support of both major parties but were vigorously opposed by the Greens, stripped the act of its basic human rights protections.

She said the amended act contradicted one of the key recommendations of the Expert Panel on Asylum Seekers, which was chaired by retired defence chief Angus Houston.

"The High Court has been clear that regional processing must meet the international human rights standards previously set out in the Migration Act," Prof Triggs said.

"In light of the amendments, there will be no opportunity for the High Court to review whether regional processing will be conducted in accordance with human rights standards.

"The repeal of human rights protections contained in the Migration Act violates one of the first recommendations of the expert panel report, that adherence by Australia to its international obligations should be one of the guiding principles shaping Australian policy on asylum seeker issues."

Prof Triggs said the commission was alarmed Australia was not required by the act to ensure regional processing countries respected the human rights of asylum seekers.

She also raised concerns about unaccompanied children arriving in Australia by boat.

"We are concerned that, under these amendments to the Migration Act, the Minister will not need to consider, on an individual basis, the best interests of unaccompanied children before sending them to a regional processing country," she said.

"The expert panel has stated that, in order to fulfil its international obligations, Australia must take into account a person's individual characteristics when deciding whether to transfer them, including the best interests of a child.

"Furthermore, the commission is deeply concerned that the principle of 'no advantage' will mean, in practice, that asylum seekers who arrive by boat may be exposed to lengthy periods of time in regional processing countries, without a durable resettlement solution."

Despite her criticism of the legislative changes, Prof Triggs praised the work of the Houston panel and its recommendations for regional co-operation and an increase to Australia's refugee intake.

She said these recommendations would help reduce the risk of further people dying at sea and urged the government to implement them as soon as possible.

But the flow of boats was showing no signs of abating, with four vessels carrying almost 200 people being intercepted on Thursday.

The asylum seekers were taken to Christmas Island, with the government unable to say on Friday whether they would end up on Nauru or PNG for processing.

Home Affairs Minister Jason Clare would only say people arriving by boat without a visa after August 13 ran the risk of being taken to another country for processing.

Meanwhile, defence reconnaissance teams touched down in PNG and Nauru on Friday to begin the task of setting up temporary processing facilities.